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Like Mike said, the tower zone gains will be set independent of the in-boat zone. Why? Because you want the tower to hit the sweet spot between low noise and high dynamic range instead of being governed by an alternate zone. You are not trying to balance it at straight up on the fader with another zone.
There are three basic tuning methods.
1) A CD or downloaded sine wave at the correct and different frequencies for fullrange speakers and subs. You would use a voltmeter to set the voltage limit of the amplifier with no speakers attached according to a formula and according to a known amplifier power at a particular impedance and at a particualr supply voltage. You want to avoid this method unless you have those accurate numbers. This works with JL Audio amplifiers because they will meet their 14.4 V spec even at 12.6 Volts. Because the JL Audio amplifiers are so conservatively rated we usually tweak this by ear afterwards. I would avoid this method unless you are given realistic, hard numbers. Otherwise you could do damage to your speakers.
2) The same CD or download with a handheld O-scope or distortion analyzer where you measure the amplifier output to the maximum pre-clipped level. Either measuring device will detect the first signs of a sinewave as it begins to square off (clipping).
3) Tuning by ear where you are the instrument that detects initial clipping/compression. In this case you are using dense and dynamic music.

Just a thought, when we tuned mine we set the Amps gains very low, like 10%-15% max, on the ZLD it has Gains on the top as well.

We adjusted these to help get the Tower and Cabins at an even volume as you turn the ZLD volume up.

I was finding with all the XM9s on the tower i would get a really light shhhh sound in my speakers, not a buzz or whistle just a smooth static noise, turning the amp gains down low and adjusting the ZLD seemed to fix this problem.

Just a thought, when we tuned mine we set the Amps gains very low, like 10%-15% max, on the ZLD it has Gains on the top as well.

We adjusted these to help get the Tower and Cabins at an even volume as you turn the ZLD volume up.

I was finding with all the XM9s on the tower i would get a really light shhhh sound in my speakers, not a buzz or whistle just a smooth static noise, turning the amp gains down low and adjusting the ZLD seemed to fix this problem.

Only problem with that is you leave power on the table. gains should be set across the board, at each device, just before the device reaches clipping. Unity gain or something like that? You are going to end up turning down your overall output on the tower, right? Can you not adjust the fade more so the towers kick on less?

Only problem with that is you leave power on the table. gains should be set across the board, at each device, just before the device reaches clipping. Unity gain or something like that? You are going to end up turning down your overall output on the tower, right? Can you not adjust the fade more so the towers kick on less?

I didnt want to get into too much detail in fear of the Audio Gods coming over the top and bashing.

The ZLD has a Gain for each input, cabin, tower, sub, so you can set the Amp gain at <exp> 15% and then adjust the gain on the ZLD up or down. The ZLD comes with its gains already set from the factory but when tuning my boat we found that the amps gains needed to be turned down and the ZLD gain adjusted as well.

You will still have to have the Frequency set on the amps, high pass, low pass, what cross over frequency. The ZLD gain is no different then amp gain.

Since the ZLD boosts the signal of your Inc head, or MP3 unit, if say the amp is at 50% gain with what would normally be a 4v signal, now its way over gained due to the ZLD putting in a 8v signal.

This is just my opinion, but I would not use the reduction of hiss as my prime objective in setting amplifier gains. My goal is to get the maximum pre-clipped power and maximum dynamic range in balance with a lowered noise floor. This is achieved through the principles of 'unity gain'. The 'hiss' can come from another upstream source or a gain inequity. So rather than clamp down on the gain on the amplifier input I would rather solve the noise where it actually originates. 'Unity gain' means a constant gain from the beginning to end of the signal path. Any inordinately low gain at one stage forces an inordinate amount of gain multiplication in the next stage. And that is where the noise (hiss) usually originates. To correctly set gains you would ideally like to start off at the first source with high gain and maintain that high gain or incrementally reduce that gain with each addition component in the signal path....but never lower the gain only to have to raise the gain in the following stage. In mobile electronics we would like to have good gain from the ipod, HU, and EQ. One weak stage will require more gain in the next stage which raises the noise floor. You don't want to allow this condition by only placing a bandaid at the very end of the signal path. There is a prescribed sequence to follow from beginning to end. You identify the maximum gain level of every audio component the same way you manage the amplifier, whether by an O-scope, distortion analyzer, detection by ear, or by measuring a known maximum output voltage with a voltmeter.
Btw, as for the 8 volts ZLD preout, that single stereo chip max voltage is split via a fader into in-boat and tower zones for a maximum of 4-volts per each zone. And 4-volts is plenty of voltage while not being out of the ordinary. What I'm saying is that this is not so much voltage that you have to over-compensate in your amplifier input gain setting.

I think I got it all, but why do these threads always go his direction.

A pic of the gains set on each amp would be fine to start with and since most have the identical equipment one could conclude that the settings could be relatively the same within the same boat.

That would be true IF all the equipment is identical and IF the system you are emmulating is tuned optimumly in the first place. IMO, there is a definitely a right and wrong way. I'm seeing this as no more than an over-simplified shortcut that will leave your system under-performing. If one route seems good enough or logical enough then follow that. You are fortuneate to get the benefit of the knowledge and experience whether or not you use it.

David, So if a moomba with an exile system was tuned properly at earmark ( couple years ago) with this same exact equipment, then your telling me, that if I configure my settings to match them it would provide an under performing system, because I didn't do it myself.

I believe there are people on here that have optimally tuned there systems going through the necessary time to clip, vm meter or o scope their settings . I however are looking at the good people of this forum to give me good advice.

Like they do with ballast upgrades, oil changes, audio, pp surf speeds etc. not sure why a shortcut means less optimal when someone else has gotten it to optimal. Why re invent the the wheel, this certainly is not rocket science. If this was a MC then certainly apples to oranges.